# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 16:45:02 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (3R)-3-phenyl-3-({[4-(4-pyridin-4-ylphenyl)thiophen-2-yl]carbonyl}amino)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](NC(=O)c1scc(c1)c2ccc(cc2)c3ccncc3)c4ccccc4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PF3  PF3  '(3R)-3-phenyl-3-({[4-(4-pyridin-4-ylphenyl)thiophen-2-yl]carbonyl}amino)propanoic acid'  ligand  50  31  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PF3
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PF3  S1    S  S2     0   0.176   1.7849  -0.7856  -0.8052
 PF3  C1    C  CR5    0  -0.243   0.2305  -0.0403  -0.8004
 PF3  C2    C  CR15   0  -0.200  -0.1969   0.1840   0.4744
 PF3  C3    C  CR5    0   0.091   0.7234  -0.2584   1.4661
 PF3  C4    C  CR15   0  -0.423   1.8431  -0.8061   0.8964
 PF3  C5    C  CR6    0   0.124   0.4991  -0.1413   2.9124
 PF3  C6    C  CR16   0  -0.347   1.5672  -0.0950   3.8102
 PF3  C7    C  CR16   0  -0.195   1.3476   0.0054   5.1721
 PF3  C8    C  CR6    0  -0.018   0.0528   0.0749   5.6884
 PF3  C9    C  CR16   0  -0.274  -1.0148   0.0352   4.7916
 PF3  C10   C  CR16   0  -0.252  -0.7955  -0.0752   3.4296
 PF3  C11   C  CR6    0   0.162  -0.1792   0.1914   7.1387
 PF3  C12   C  CR16   0  -0.339  -1.2659   0.9005   7.6489
 PF3  C13   C  CR16   0  -0.037  -1.4399   0.9813   9.0208
 PF3  N1    N  N      0  -0.429  -0.6222   0.4175   9.9027
 PF3  C14   C  CR16   0  -0.091   0.4145  -0.2578   9.4193
 PF3  C15   C  CR16   0  -0.352   0.6768  -0.4003   8.0665
 PF3  C16   C  C      0   0.525  -0.5280   0.3250  -2.0200
 PF3  O1    O  O      0  -0.468  -1.4650   1.1079  -1.9425
 PF3  N2    N  NH1    0  -0.673  -0.1202  -0.2495  -3.1638
 PF3  C17   C  CH1    0  -0.103  -0.7620  -0.0369  -4.4557
 PF3  C18   C  CH2    0  -0.607  -1.5580  -1.2681  -4.8754
 PF3  C19   C  C      0   0.435  -2.3236  -1.0750  -6.1969
 PF3  O2    O  O      0  -0.544  -2.7063   0.0827  -6.4563
 PF3  O3    O  OC    -1  -0.650  -2.5280  -2.0983  -6.8790
 PF3  C20   C  CR6    0   0.306   0.2845   0.3730  -5.4680
 PF3  C21   C  CR16   0  -0.289   0.3798   1.6996  -5.8756
 PF3  C22   C  CR16   0  -0.269   1.3596   2.1014  -6.7740
 PF3  C23   C  CR16   0  -0.285   2.2620   1.1741  -7.2792
 PF3  C24   C  CR16   0  -0.238   2.1748  -0.1531  -6.8800
 PF3  C25   C  CR16   0  -0.375   1.1922  -0.5493  -5.9821
 PF3  H2    H  HCR5   0   0.273  -1.1407   0.6618   0.6959
 PF3  H4    H  HCR5   0   0.327   2.7003  -1.2323   1.3952
 PF3  H6    H  HCR6   0   0.217   2.5864  -0.1171   3.4449
 PF3  H7    H  HCR6   0   0.268   2.2008   0.0604   5.8362
 PF3  H9    H  HCR6   0   0.259  -2.0338   0.0660   5.1565
 PF3  H10   H  HCR6   0   0.262  -1.6492  -0.1288   2.7662
 PF3  H12   H  HCR6   0   0.265  -1.9646   1.4047   6.9947
 PF3  H13   H  HCR6   0   0.250  -2.2807   1.5354   9.4234
 PF3  H14   H  HCR6   0   0.280   1.0760  -0.7174  10.1456
 PF3  H15   H  HCR6   0   0.253   1.5330  -0.9821   7.7514
 PF3  HA    H  HNH1   0   0.381   0.5613  -0.9919  -3.1226
 PF3  H17   H  HCH1   0   0.258  -1.4564   0.7907  -4.3280
 PF3  H181  H  HCH2   0   0.222  -2.2888  -1.4809  -4.0868
 PF3  H182  H  HCH2   0   0.195  -0.9128  -2.1493  -4.9326
 PF3  H21   H  HCR6   0   0.221  -0.3227   2.4276  -5.4877
 PF3  H22   H  HCR6   0   0.206   1.4160   3.1374  -7.0826
 PF3  H23   H  HCR6   0   0.268   3.0267   1.4825  -7.9806
 PF3  H24   H  HCR6   0   0.257   2.8718  -0.8837  -7.2704
 PF3  H25   H  HCR6   0   0.221   1.1383  -1.5914  -5.6888

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PF3  S1   C1    aromatic  1.724  0.020  1.724
 PF3  S1   C4    aromatic  1.703  0.020  1.703
 PF3  C1   C2    aromatic  1.363  0.020  1.363
 PF3  C1   C16   single    1.482  0.020  1.482
 PF3  C2   C3    aromatic  1.423  0.020  1.423
 PF3  C2   H2    single    0.930  0.020  1.080
 PF3  C3   C4    aromatic  1.371  0.020  1.371
 PF3  C3   C5    single    1.468  0.020  1.468
 PF3  C4   H4    single    0.930  0.020  1.080
 PF3  C5   C6    aromatic  1.396  0.020  1.396
 PF3  C5   C10   aromatic  1.396  0.020  1.396
 PF3  C6   C7    aromatic  1.383  0.020  1.383
 PF3  C6   H6    single    0.930  0.020  1.080
 PF3  C7   C8    aromatic  1.396  0.020  1.396
 PF3  C7   H7    single    0.930  0.020  1.080
 PF3  C8   C9    aromatic  1.395  0.020  1.395
 PF3  C8   C11   single    1.473  0.020  1.473
 PF3  C9   C10   aromatic  1.384  0.020  1.384
 PF3  C9   H9    single    0.930  0.020  1.080
 PF3  C10  H10   single    0.930  0.020  1.080
 PF3  C11  C12   aromatic  1.394  0.020  1.394
 PF3  C11  C15   aromatic  1.394  0.020  1.394
 PF3  C12  C13   aromatic  1.385  0.020  1.385
 PF3  C12  H12   single    0.930  0.020  1.080
 PF3  C13  N1    aromatic  1.328  0.020  1.328
 PF3  C13  H13   single    0.930  0.020  1.080
 PF3  N1   C14   aromatic  1.328  0.020  1.328
 PF3  C14  C15   aromatic  1.385  0.020  1.385
 PF3  C14  H14   single    0.930  0.020  1.080
 PF3  C15  H15   single    0.930  0.020  1.080
 PF3  C16  O1    double    1.224  0.020  1.224
 PF3  C16  N2    single    1.343  0.020  1.343
 PF3  N2   C17   single    1.458  0.020  1.458
 PF3  N2   HA    single    0.860  0.020  1.020
 PF3  C17  C18   single    1.525  0.020  1.525
 PF3  C17  C20   single    1.513  0.020  1.513
 PF3  C17  H17   single    0.970  0.020  1.090
 PF3  C18  C19   single    1.539  0.020  1.539
 PF3  C18  H181  single    0.970  0.020  1.090
 PF3  C18  H182  single    0.970  0.020  1.090
 PF3  C19  O2    deloc     1.247  0.020  1.247
 PF3  C19  O3    deloc     1.247  0.020  1.247
 PF3  C20  C21   aromatic  1.391  0.020  1.391
 PF3  C20  C25   aromatic  1.392  0.020  1.392
 PF3  C21  C22   aromatic  1.389  0.020  1.389
 PF3  C21  H21   single    0.930  0.020  1.080
 PF3  C22  C23   aromatic  1.389  0.020  1.389
 PF3  C22  H22   single    0.930  0.020  1.080
 PF3  C23  C24   aromatic  1.389  0.020  1.389
 PF3  C23  H23   single    0.930  0.020  1.080
 PF3  C24  C25   aromatic  1.389  0.020  1.389
 PF3  C24  H24   single    0.930  0.020  1.080
 PF3  C25  H25   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PF3  C4    S1   C1     91.91  3.000
 PF3  C16   C1   C2    124.65  3.000
 PF3  C16   C1   S1    124.46  3.000
 PF3  C2    C1   S1    110.88  3.000
 PF3  H2    C2   C3    124.00  3.000
 PF3  H2    C2   C1    122.56  3.000
 PF3  C3    C2   C1    113.43  3.000
 PF3  C5    C3   C4    124.48  3.000
 PF3  C5    C3   C2    124.24  3.000
 PF3  C4    C3   C2    111.27  3.000
 PF3  H4    C4   C3    127.91  3.000
 PF3  H4    C4   S1    119.59  3.000
 PF3  C3    C4   S1    112.50  3.000
 PF3  C10   C5   C6    118.02  3.000
 PF3  C10   C5   C3    120.70  3.000
 PF3  C6    C5   C3    121.28  3.000
 PF3  H6    C6   C7    118.88  3.000
 PF3  H6    C6   C5    120.16  3.000
 PF3  C7    C6   C5    120.94  3.000
 PF3  H7    C7   C8    120.11  3.000
 PF3  H7    C7   C6    118.85  3.000
 PF3  C8    C7   C6    121.01  3.000
 PF3  C11   C8   C9    120.97  3.000
 PF3  C11   C8   C7    120.95  3.000
 PF3  C9    C8   C7    118.08  3.000
 PF3  H9    C9   C10   118.88  3.000
 PF3  H9    C9   C8    120.19  3.000
 PF3  C10   C9   C8    120.91  3.000
 PF3  H10   C10  C9    118.82  3.000
 PF3  H10   C10  C5    120.14  3.000
 PF3  C9    C10  C5    121.03  3.000
 PF3  C15   C11  C12   116.80  3.000
 PF3  C15   C11  C8    121.65  3.000
 PF3  C12   C11  C8    121.54  3.000
 PF3  H12   C12  C13   119.38  3.000
 PF3  H12   C12  C11   121.27  3.000
 PF3  C13   C12  C11   119.34  3.000
 PF3  H13   C13  N1    116.59  3.000
 PF3  H13   C13  C12   119.67  3.000
 PF3  N1    C13  C12   123.74  3.000
 PF3  C14   N1   C13   117.04  3.000
 PF3  H14   C14  C15   119.66  3.000
 PF3  H14   C14  N1    116.60  3.000
 PF3  C15   C14  N1    123.74  3.000
 PF3  H15   C15  C14   119.31  3.000
 PF3  H15   C15  C11   121.35  3.000
 PF3  C14   C15  C11   119.33  3.000
 PF3  N2    C16  O1    124.06  3.000
 PF3  N2    C16  C1    116.10  3.000
 PF3  O1    C16  C1    119.84  3.000
 PF3  HA    N2   C17   116.16  3.000
 PF3  HA    N2   C16   119.02  3.000
 PF3  C17   N2   C16   123.95  3.000
 PF3  H17   C17  C20   108.30  3.000
 PF3  H17   C17  C18   108.26  3.000
 PF3  C20   C17  C18   113.31  3.000
 PF3  H17   C17  N2    106.73  3.000
 PF3  C20   C17  N2    109.14  3.000
 PF3  C18   C17  N2    110.85  3.000
 PF3  H182  C18  H181  105.94  3.000
 PF3  H182  C18  C19   110.47  3.000
 PF3  H181  C18  C19   108.08  3.000
 PF3  H182  C18  C17   110.91  3.000
 PF3  H181  C18  C17   107.86  3.000
 PF3  C19   C18  C17   113.24  3.000
 PF3  O3    C19  O2    126.74  3.000
 PF3  O3    C19  C18   116.63  3.000
 PF3  O2    C19  C18   116.60  3.000
 PF3  C25   C20  C21   118.61  3.000
 PF3  C25   C20  C17   121.24  3.000
 PF3  C21   C20  C17   120.13  3.000
 PF3  H21   C21  C22   119.65  3.000
 PF3  H21   C21  C20   119.43  3.000
 PF3  C22   C21  C20   120.92  3.000
 PF3  H22   C22  C23   120.09  3.000
 PF3  H22   C22  C21   119.87  3.000
 PF3  C23   C22  C21   120.04  3.000
 PF3  H23   C23  C24   120.19  3.000
 PF3  H23   C23  C22   120.29  3.000
 PF3  C24   C23  C22   119.52  3.000
 PF3  H24   C24  C25   119.75  3.000
 PF3  H24   C24  C23   120.06  3.000
 PF3  C25   C24  C23   120.19  3.000
 PF3  H25   C25  C24   118.97  3.000
 PF3  H25   C25  C20   120.30  3.000
 PF3  C24   C25  C20   120.73  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PF3  CONST_01  C3   C2   C1   S1      0.00   0.0  0
 PF3  CONST_02  C2   C3   C4   S1      0.00   0.0  0
 PF3  CONST_03  C5   C3   C4   S1    180.00   0.0  0
 PF3  CONST_04  C3   C4   S1   C1      0.00   0.0  0
 PF3  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 PF3  CONST_06  C5   C3   C2   C1    180.00   0.0  0
 PF3  CONST_07  C4   S1   C1   C2      0.00   0.0  0
 PF3  CONST_10  C7   C6   C5   C3    180.00   0.0  0
 PF3  CONST_11  C9   C10  C5   C3    180.00   0.0  0
 PF3  CONST_14  C8   C7   C6   C5      0.00   0.0  0
 PF3  CONST_15  C8   C9   C10  C5      0.00   0.0  0
 PF3  CONST_16  C9   C10  C5   C6      0.00   0.0  0
 PF3  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 PF3  CONST_18  C11  C8   C7   C6    180.00   0.0  0
 PF3  CONST_19  C10  C5   C6   C7      0.00   0.0  0
 PF3  CONST_20  C10  C9   C8   C7      0.00   0.0  0
 PF3  CONST_23  C13  C12  C11  C8    180.00   0.0  0
 PF3  CONST_24  C14  C15  C11  C8    180.00   0.0  0
 PF3  CONST_27  C11  C8   C9   C10   180.00   0.0  0
 PF3  CONST_28  N1   C13  C12  C11     0.00   0.0  0
 PF3  CONST_29  N1   C14  C15  C11     0.00   0.0  0
 PF3  CONST_30  C14  C15  C11  C12     0.00   0.0  0
 PF3  CONST_31  C14  N1   C13  C12     0.00   0.0  0
 PF3  CONST_32  C15  C11  C12  C13     0.00   0.0  0
 PF3  CONST_33  C15  C14  N1   C13     0.00   0.0  0
 PF3  CONST_34  C23  C22  C21  C20     0.00   0.0  0
 PF3  CONST_35  C23  C24  C25  C20     0.00   0.0  0
 PF3  CONST_36  C24  C25  C20  C21     0.00   0.0  0
 PF3  CONST_37  C24  C23  C22  C21     0.00   0.0  0
 PF3  CONST_38  C25  C20  C21  C22     0.00   0.0  0
 PF3  CONST_39  C25  C24  C23  C22     0.00   0.0  0
 PF3  CONST_40  C16  C1   C2   C3    180.00   0.0  0
 PF3  CONST_41  C16  C1   S1   C4    180.00   0.0  0
 PF3  CONST_42  C22  C21  C20  C17   180.00   0.0  0
 PF3  CONST_43  C24  C25  C20  C17   180.00   0.0  0
 PF3  CONST_44  H2   C2   C1   S1    180.00   0.0  0
 PF3  CONST_45  H4   C4   S1   C1    180.00   0.0  0
 PF3  CONST_46  H6   C6   C5   C3      0.00   0.0  0
 PF3  CONST_47  H10  C10  C5   C3      0.00   0.0  0
 PF3  CONST_48  H7   C7   C6   C5    180.00   0.0  0
 PF3  CONST_49  H9   C9   C10  C5    180.00   0.0  0
 PF3  CONST_50  H12  C12  C11  C8      0.00   0.0  0
 PF3  CONST_51  H15  C15  C11  C8      0.00   0.0  0
 PF3  CONST_52  H13  C13  C12  C11   180.00   0.0  0
 PF3  CONST_53  H14  C14  C15  C11   180.00   0.0  0
 PF3  CONST_54  H22  C22  C21  C20   180.00   0.0  0
 PF3  CONST_55  H24  C24  C25  C20   180.00   0.0  0
 PF3  CONST_56  H25  C25  C20  C21   180.00   0.0  0
 PF3  CONST_57  H23  C23  C22  C21   180.00   0.0  0
 PF3  CONST_58  H21  C21  C22  C23   180.00   0.0  0
 PF3  CONST_59  C17  N2   C16  C1    180.00   0.0  0
 PF3  CONST_60  HA   N2   C16  C1      0.00   0.0  0
 PF3  CONST_61  C17  N2   C16  O1      0.00   0.0  0
 PF3  Var_01    O1   C16  C1   S1   -163.53  30.0  2
 PF3  Var_02    O2   C19  C18  C17   -30.35  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PF3  chir_01  C17  N2  C18  C20  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PF3  plan-1  S1   0.020
 PF3  plan-1  C1   0.020
 PF3  plan-1  C2   0.020
 PF3  plan-1  C3   0.020
 PF3  plan-1  C4   0.020
 PF3  plan-1  C5   0.020
 PF3  plan-1  C16  0.020
 PF3  plan-1  H2   0.020
 PF3  plan-1  H4   0.020
 PF3  plan-2  C3   0.020
 PF3  plan-2  C5   0.020
 PF3  plan-2  C6   0.020
 PF3  plan-2  C7   0.020
 PF3  plan-2  C8   0.020
 PF3  plan-2  C9   0.020
 PF3  plan-2  C10  0.020
 PF3  plan-2  C11  0.020
 PF3  plan-2  H6   0.020
 PF3  plan-2  H7   0.020
 PF3  plan-2  H9   0.020
 PF3  plan-2  H10  0.020
 PF3  plan-3  C8   0.020
 PF3  plan-3  C11  0.020
 PF3  plan-3  C12  0.020
 PF3  plan-3  C13  0.020
 PF3  plan-3  N1   0.020
 PF3  plan-3  C14  0.020
 PF3  plan-3  C15  0.020
 PF3  plan-3  H12  0.020
 PF3  plan-3  H13  0.020
 PF3  plan-3  H14  0.020
 PF3  plan-3  H15  0.020
 PF3  plan-4  C17  0.020
 PF3  plan-4  C20  0.020
 PF3  plan-4  C21  0.020
 PF3  plan-4  C22  0.020
 PF3  plan-4  C23  0.020
 PF3  plan-4  C24  0.020
 PF3  plan-4  C25  0.020
 PF3  plan-4  H21  0.020
 PF3  plan-4  H22  0.020
 PF3  plan-4  H23  0.020
 PF3  plan-4  H24  0.020
 PF3  plan-4  H25  0.020
 PF3  plan-5  C1   0.020
 PF3  plan-5  C16  0.020
 PF3  plan-5  O1   0.020
 PF3  plan-5  N2   0.020
 PF3  plan-5  C17  0.020
 PF3  plan-5  HA   0.020
 PF3  plan-6  C18  0.020
 PF3  plan-6  C19  0.020
 PF3  plan-6  O2   0.020
 PF3  plan-6  O3   0.020

